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23 citation(s) found for "Xiao, Yan".

Abstract 531: Mutagenic Gene Trapping to Study Novel Genes in Zebrafish Cardiovascular Development
El‐Rass, Suzan , Eisa-Beygi, Shahram, Liu, Xiaohua , Mauro, Antonio , Wang, Youdong , Plant, Pamela , Liu, Xiao-hua, Zhang, Haibo , Clark, Karl J. , Ekker, Stephen C. , Wen, Xiao‐Yan

Arteriosclerosis, Thrombosis, and Vascular Biology | July 3, 2021 | Volume: 34 | Issue: suppl_1 | Pages: No page available

10.1161/atvb.34.suppl_1.531 Get It

The zebrafish has emerged as an excellent model for cardiovascular research thanks to its ex-utero and rapid embryonic development, its embryonic transparent nature, and its capacity to survive in the absence of a functional cardiovascular system during the first week of development, which enables functional characterization of mutations that would otherwise induce lethality in traditional murine models. The aim of this project is to identify and characterize novel genes involved in zebrafish cardiovascular development using mutagenic gene trapping, a technique that generates random insertional mutations across the genome. We use the well-defined RP2 gene-breaking transposon system, which not only mutates, but also fluorescently tags the trapped gene product(s) (Clark, Nat Methods, 2011). RP2 also introduces loxP sites into the mutant locus, which can be used for Cre-mediated phenotype rescue by microinjection of Cre recombinase, or by crossing to tissue-specific Cre lines. From over 3000 RP2-injected embryos, 141 fish showed germline transmission. Among them, 51 expressed strong fluorescence in different tissues, including the heart, vessels, notochord, central nervous system (CNS), and eyes. Three cardiovascular lines were selected for phenotypic characterization and functional studies. RP2#C2 strain expressed fluorescence in the heart valves, CNS, eyes and pectoral fin buds. Inverse PCR in RP2#C2 demonstrated a trapped gene at meis4.1a, which encodes a homeobox transcription factor that has not been previously studied in zebrafish. RP2#121 strain expressed strong fluorescence in cardiac and skeletal muscles. RP2#91 strain showed expression in the vasculature and demonstrated a trapped gene at pdgfra. Homozygous RP2#91 mutants showed severe defects in the heart, blood flow, and other body parts including the head and musculature. We are currently creating a panel of tissue-specific Cre lines targeting tissues such as cardiomyocytes, endothelial cells and smooth muscle cells for spatiotemporal rescuing of the mutant phenotype. The generated zebrafish protein-trap lines are invaluable tools to annotate gene function, dissect the molecular mechanisms of cardiovascular development, and potentially serve as disease models.
Higher-order connections between stereotyped subsets: implications for improved patient classification in CLL
Agathangelidis, Andreas , Chatzidimitriou, Anastasia , Gemenetzi, Katerina , Giudicelli, Véronique , Karypidou, Maria, Plevová, Karla , Davis, Zadie , Yan, Xiao‐Jie , Jeromin, Sabine , Schneider, Christof , Pedersen, Lone Bredo , Tschumper, Renee C. , Sutton, Lesley‐Ann, Gastel, Ellen J. van, Armand, Marine , Tausch, Eugen , Baer, Constance , Navarro, Alba , Septenville, Anne Langlois de, Guido, Valentina, Mitterbauer‐Hohendanner, Gerlinde, Brieghel, Christian , Lawless, Sarah, Meggendorfer, Manja , Brázdilová, Kamila, Ritgen, Matthias , Facco, Monica , Tresoldi, Cristina , Visentin, Andrea , Patriarca, Andrea , Catherwood, Mark , Bonello, Lisa, Sudarikov, Andrey , Roumelioti, Maria, Francová, Hana Skuhrová, Moysiadis, Theodoros , Giannopoulos, Krzysztof , Mansouri, Larry, Karan-Djurašević, Teodora , Sandaltzopoulos, Raphael , Fais, Franco , Kater, Arnon P. , Panovska, Irina, Rossi, Davide , Alshemmari, Salem , Costeas, Paul , Espinet, Blanca , Antić, Darko , Foroni, Letizia, Montillo, Marco , Trentin, Livio , Stavroyianni, Niki, Gaïdano, Gianluca , Celle, Paola Francia di, Niemann, Carsten Utoft , Anagnostopoulos, Αchilles , Pott, Christiane , Fischer, Kirsten , Hallek, Michael , Oscier, David , Jelinek, Diane F., Lefranc, Marie‐Paule , Belessi, Chrysoula, Davi, Frédéric , Rosenquist, Richard , Σταματόπουλος, Κώστας , Jelinek, Diane, Gaidano, Gianluca , Rosenquist, Richard , Espinet, Blanca , Baliakas, Panagiotis , Scarfò, Lydia , Biderman, Bella V. , Bagnara, Davide , Guido, Valentina, Dimovski, Aleksandar J , Vanura, Katrina , Veronese, Silvio , Bödör, Csaba , Panagiotidis, Panagiotis T. , Campo, Elı́as , Stilgenbauer, Stephan , Haferlach, Claudia , Chiorazzi, Nicholas , Pospı́šilová, Šárka , Kossida, Sofia , Langerak, Anton W. , Ghia, Paolo

Blood | September 29, 2020 | Volume: 137 | Issue: 10 | Pages: 1365-1376

10.1182/blood.2020007039 | PMID 32992344 Get It

Abstract Chronic lymphocytic leukemia (CLL) is characterized by the existence of subsets of patients with (quasi)identical, stereotyped B-cell receptor (BcR) immunoglobulins. Patients in certain major stereotyped subsets often display remarkably consistent clinicobiological profiles, suggesting that the study of BcR immunoglobulin stereotypy in CLL has important implications for understanding disease pathophysiology and refining clinical decision-making. Nevertheless, several issues remain open, especially pertaining to the actual frequency of BcR immunoglobulin stereotypy and major subsets, as well as the existence of higher-order connections between individual subsets. To address these issues, we investigated clonotypic IGHV-IGHD-IGHJ gene rearrangements in a series of 29 856 patients with CLL, by far the largest series worldwide. We report that the stereotyped fraction of CLL peaks at 41% of the entire cohort and that all 19 previously identified major subsets retained their relative size and ranking, while 10 new ones emerged; overall, major stereotyped subsets had a cumulative frequency of 13.5%. Higher-level relationships were evident between subsets, particularly for major stereotyped subsets with unmutated IGHV genes (U-CLL), for which close relations with other subsets, termed “satellites,” were identified. Satellite subsets accounted for 3% of the entire cohort. These results confirm our previous notion that major subsets can be robustly identified and are consistent in relative size, hence representing distinct disease variants amenable to compartmentalized research with the potential of overcoming the pronounced heterogeneity of CLL. Furthermore, the existence of satellite subsets reveals a novel aspect of repertoire restriction with implications for refined molecular classification of CLL.
Building the vertebrate codex using the gene breaking protein trap library
Ichino, Noriko , Serres, MaKayla R., Urban, Rhianna , Urban, Mark D. , Treichel, Anthony J. , Schaefbauer, Kyle, Tallant, Lauren , Varshney, Gaurav K. , Skuster, Kimberly J., McNulty, Melissa S. , Daby, Camden L. , Wáng, Ying , Liao, Hsin‐Kai, El‐Rass, Suzan , Liu, Weibin , Anderson, Jennifer L. , Wishman, Mark , Sabharwal, Ankit , Schimmenti, Lisa A. , Sivasubbu, Sridhar , Balciunas, Darius , Hammerschmidt, Matthias , Farber, Steven , Wen, Xiao‐Yan , McGrail, Maura , Burgess, Shawn M. , Ekker, Stephen C. , Urban, Rhianna M , Schaefbauer, Kyle J., Tallant, Lauren E., Ding, Yonghe , Wishman, Mark D, Sabharwal, Ankit , Balciunas, Darius , Hammerschmidt, Matthias , Farber, Steven Arthur , Lin, Xueying , McGrail, Maura , Essner, Jeffrey , Burgess, Shawn M , Clark, Karl J , Ekker, Stephen C , Wen, Xiao-Yan , Schimmenti, Lisa A , Treichel, Anthony J , Ichino, Noriko , Xu, Xiaolei , Essner, Jeffrey J. , Clark, Karl J.

eLife | August 11, 2020 | Volume: 9 | Issue: No issue available | Pages: No page available

10.7554/elife.54572 | PMID 32779569 Get It

One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b , fras1 , tnnt2a , edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated genes with 40 as potential new disease models. Severely reduced skeletal muscle Ca 2+ transients in GBT ryr1b homozygous animals validated the ability to explore molecular mechanisms of genetic diseases. This GBT system facilitates novel functional genome annotation towards understanding cellular and molecular underpinnings of vertebrate biology and human disease.
Studies of the Bcl Inhibitor GX15-070 in Multiple Myeloma Demonstrate Substantial Pre-Clinical Activity.
Stewart, A. Keith , Rauw, Jennifer , Pathangey, Latha , Trudel, Suzanne , Li, Zhi Hua, Wen, Xiao‐Yan , Bergsagel, P. Leif

Blood | April 19, 2020 | Volume: 106 | Issue: 11 | Pages: 1572-1572

10.1182/blood.v106.11.1572.1572 Get It

Abstract GX15-070 is a small-molecule antagonist of the BH3-binding groove of the Bcl-2 family of proteins and can thus induce apoptosis by inhibiting the interaction between pro- and anti-apoptotic proteins. In addition, GX15-070 activates a cellular pathway, which leads to the activation of the pro-apoptotic BH3-only protein Bim, a natural cellular inhibitor of anti-apoptotic members. Together, the direct inhibition of anti-apoptotic Bcl-2 family proteins and the activation of pro-apoptotic Bim by GX15-070 can sensitize tumor cells to apoptosis. Bcl-2 family members, particularly Bcl-XL and Mcl-1 have been implicated in the survival of myeloma cells and may be responsible, in part, for drug resistance. Consequently, GX15-070 was tested against the MMRC 12 validation cell line panel, a panel of 12 standardized and annotated human myeloma cell lines (HMCLs). Western blots preformed on 8 HMCLs confirmed expression of Bcl-2, Mcl-1 and/or Bcl-XL. Basal levels of Bcl-2 and MCl-1 were relatively similar across all HMCLs studied whereas levels of Bcl-XL were variable GX15-070 inhibited the viability of all 12 myeloma cell lines as determined by MTT assay. The mean IC50 was 215 nM; range (6.4-678nM) and sensitivity did not correlate with level of Bcl-2, MCL-1 or Bcl-XL expression. On the other hand cytotoxicity to normal human blood lymphocytes, stroma and bone marrow CFUs was not observed at concentrations which were effectively cytotoxic to HMCL. Time course experiments demonstrate that apoptosis and cleavage of caspase 3 began by 12 hours and continued to increase over a 96 hour period. Co-culture with human bone marrow stroma cells (BMSCs) failed to protect HMCL from GX15-070 induced cytotoxicity. Similarly, potent MM growth factors, Interleukin 6 (IL-6) and Insulin like growth factor (IGF)-1 did not confer resistance to GX15-070. Of interest, overexpression of Bcl-2 has been shown to attenuate PS-341-induced cell death (Mitisades); however, the combination of PS-341 and GX15-070 did not reveal synergistic interaction in preliminary results. Studies looking at other drug combinations are planned. Finally, GX15-070 produced cytotoxic responses in the first primary myeloma sample tested with further testing ongoing. Mouse xenograft studies are also ongoing and will be presented. These studies indicate extensive pre-clinical activity of GX15-070 in multiple myeloma and set the stage for planned Phase II clinical trials.
Genetic Disruption of the SH3 and SAM Domains of HACS1 Enhances Adaptive Immunity.
Wang, Dingyan , Stewart, Alex , Zhuang, Lihua, Xiao, Nancy, Hlaing, Mawmaw, Shi, Chang‐Xin, Zhu, Yuanxiao, Wang, Youdong , Stewart, A. Keith, Hlaing, Maw Maw, Wen, Xiao‐Yan

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 2299-2299

10.1182/blood.v110.11.2299.2299 Get It

Abstract HACS1 is a SH3 (Src homology 3) and SAM (sterile alpha motif) domain containing adaptor protein that is expressed in activated B and dendritic cells, is up-regulated by Interleukin 4 in the process of B cell activation and likely serves to dampen the immune response. To elucidate the function of HACS1, we generated HACS1 gene knockout mice by deletion of the SH3 and SAM domains. HACS1−/− mice were viable and fertile and had normal bone marrow B cell development and normal splenic T and B cell populations. However, adult HACS1−/− mice had increased numbers of peritoneal B1 cells (IgM+CD5+). Upon LPS plus BCR or TCR stimulations, splenic cells from HACS1−/− mice demonstrated an upregulation of activation markers with increased intensity of CD23 expression or increased population of CD69 positive cells. Purified B220+ splenic B cells from HACS1−/− mice showed increased cell proliferation upon BCR stimulation. Both T helper type 1 (Th1) and T helper type 2 (Th2) humoral responses were enhanced in HACS1−/− mice upon immunization with T cell-dependent antigen NP-KLH, which resulted in increased production of interferon-gamma (IFN-γ), anti-NP IgG2a and IL-4, as well as anti-NP IgG1 and IgE. Upon immunization with T cell-independent antigens such as TNP-LPS and TNP-Ficoll, HACS1−/− mice had increased production of anti-TNP IgM and IgG3 as compared to normal controls. The in vitro maturation of bone marrow-derived dentritic cells from HACS1−/− mice was similar to wild-type mice but HACS1−/− dentritic cells showed increased IL-12 production upon stimulation with anti-CD40 or LPS. There was no significant difference in antigen uptake by cultured dentritic cells from non-immunized wild-type or knockout mice. However, in immunized mice, an increase in antigen uptake in HACS1−/− dentritic cells was observed. We further demonstrate that the HACS1−/− B cells had increased tyrosine phosphorylation in the resting state. As deletion of the SH3 & SAM domains of HACS1 appears to generate a hypersensitive immune response, our results collectively support that HACS1 negatively regulates adaptive immunity.
CLL with Mutated IGHV4-34 Antigen Receptors Is Clinically Heterogeneous: Antigen Receptor Stereotypy Makes the Difference
Xochelli, Aliki , Hadzidimitriou, Anastasia , Sutton, Lesley‐Ann, Minga, Eva, Tausch, Eugen , Yan, Xiao‐Jie , Boudjogra, Myriam, Davis, Zadie , Sandberg, Yorick , Stavroyianni, Niki, Sudarikov, Andrey , Catherwood, Mark , Kienle, Dirk, Chatzouli, Maria, Facco, Monica , Bahlo, Jasmin, Pedersen, Lone Bredo , Mansouri, Larry, Smedby, Karin E. , Chu, Charles C. , Lefranc, Marie‐Paule , Juliusson, Gunnar , Antić, Darko , Montillo, Marco , Darzentas, Nikos , Pospı́šilová, Šárka , Hallek, Michael , Oscier, David , Belessi, Chrysoula, Jelinek, Diane F., Davi, Frédéric , Baliakas, Panagiotis , Agathangelidis, Andreas , Shanafelt, Tait D. , Plevová, Karla , Rossi, Davide , Navarro, Alba , Vojdeman, Fie Juhl , Scarfò, Lydia , Veronese, Silvio , Τζένου, Τατιάνα , Karan-Djurašević, Teodora , Giudicelli, Véronique , Panagiotidis, Panagiotis T. , Anagnostopoulos, Αchilles , Trentin, Livio , Niemann, Carsten Utoft , Döhner, Hartmut , Langerak, Anton W. , Campo, Elı́as , Chiorazzi, Nicholas , Gaïdano, Gianluca , Stilgenbauer, Stephan , Rosenquist, Richard , Ghia, Paolo , Σταματόπουλος, Κώστας

Blood | November 17, 2019 | Volume: 126 | Issue: 23 | Pages: 5263-5263

10.1182/blood.v126.23.5263.5263 Get It

Abstract The IGHV4-34 gene is very frequent (~10%) in the B cell receptor immunoglobulin (BcR IG) gene repertoire of chronic lymphocytic leukemia (CLL). Over 30% of IGHV4-34 CLL cases can be assigned to different subsets with stereotyped BcR IG. The largest is subset #4 which represents ~1% of all CLL and ~10% of IGHV4-34 CLL and is considered a prototype for indolent disease. The BcR IG of a great majority (~85%) of IGHV4-34 CLL cases carry a significant load of somatic hypermutation (SHM), often with distinctive SHM patterns. This holds especially true for stereotyped subsets and is suggestive of particular modes of interactions with the selecting antigen(s). In detail, subsets #4 and #16, both involving IgG-switched cases (IgG-CLL), exhibit the greatest sequence similarity in SHM profiles, whereas they differ in this respect from IgM/D subsets #29 and #201. Prompted by these observations, here we explored the extent that these subset-biased SHM profiles in different IGHV4-34 stereotyped subsets were reflected in distinct demographics, clinical presentation, genomic aberrations and outcomes. Within a multi-institutional series of 20,331 CLL patients, 1790 (8.8%) expressed IGHV4-34 BcR IG. Following established bioinformatics approaches for the identification of BcR IG stereotypy, 573/1790 IGHV4-34 CLL cases (32%) were assigned to stereotyped subsets; of these, 340 cases (19% of all IGHV4-34 CLL and 60% of stereotyped IGHV4-34 cases) belonged to subsets #4, #16, #29 and #201, all concerning IGHV-mutated CLL (M-CLL). Clinicobiological information was available for 275/340 patients: #4, n=150; #16, n=44; #29, n=39; and #201, n=42. Comparisons between subsets revealed no differences in gender and age distribution. Interestingly, however, 36-43% of each subset cases were young for CLL (defined as patients aged ≤55 years), which is higher compared to general CLL cohorts, where young patients generally account for ~25% of cases. In contrast, significant differences were identified between subsets regarding: (i) disease stage at diagnosis, with >90% of IgG subsets #4 and #16 diagnosed at Binet stage A versus 83% in subset #201 and 74% in subset #29 (p=0.029); (ii) CD38 expression, ranging from 1% in subset #4 to 10% in subset #201 (p=0.013); (iii) the distribution of del(13q), peaking at a remarkable 92% in subset #29 versus only 37% in subset #16 (p<0.0001). Regarding other genomic aberrations, they were either absent (NOTCH1 mutations) or rare (SF3B1 mutations, trisomy 12, del(11q), TP53 aberrations due to either del(17p) and/or TP53 mutations). The sole exception concerned a high frequency (14%) of TP53 aberrations in subset #29 (p<0.05 compared with the other subsets), which is notable for M-CLL cases in general. Time to first treatment (TTFT) could be analyzed in 228 cases. IgG subsets #4 and #16 had significantly (p=0.036) longer TTFT (median TTFT: not yet reached) compared to the IgM/D subsets #29 and #201 (median TTFT: 11 and 12 years, respectively). In conclusion, we have identified distinct clinicobiological profiles for different stereotyped IGHV4-34 M-CLL subsets, highlighting subsets #4 and #16 as particularly indolent, which is important for both medical and social reasons, especially considering that a significant proportion of patients in these subsets are diagnosed at younger ages. Our findings support the notion that BcR IG stereotypy refines prognostication in CLL, superseding the crude immunogenetic distinction based on SHM load only. Additionally, the observed heterogeneity suggests that not all M-CLL are equal, prompting further research into the underlying biological background with the ultimate aim of tailored patient management. Disclosures Tausch: Gilead: Other: Travel support. Shanafelt:Glaxo-Smith_Kline: Research Funding; Genentech: Research Funding; Celgene: Research Funding; Polyphenon E Int'l: Research Funding; Hospira: Research Funding; Janssen: Research Funding; Pharmactckucs: Research Funding; Cephalon: Research Funding. Niemann:Gilead: Consultancy; Janssen: Consultancy; Roche: Consultancy; Novartis: Other: Travel grant. Langerak:InVivoScribe: Patents & Royalties: Licensing of IP and Patent on BIOMED-2-based methods for PCR-based Clonality Diagnostics.; DAKO: Patents & Royalties: Licensing of IP and Patent on Split-Signal FISH. Royalties for Dept. of Immunology, Erasmus MC, Rotterdam, NL; Roche: Other: Lab services in the field of MRD diagnostics provided by Dept of Immunology, Erasmus MC (Rotterdam). Hallek:Celgene: Honoraria, Other: Speakers Bureau and/or Advisory Boards, Research Funding; AbbVie: Honoraria, Other: Speakers Bureau and/or Advisory Boards, Research Funding; Roche: Honoraria, Other: Speakers Bureau and/or Advisory Boards, Research Funding; Boehringher Ingelheim: Honoraria, Other: Speakers Bureau and/or Advisory Boards; Pharmacyclics: Honoraria, Other: Speakers Bureau and/or Advisory Boards, Research Funding; Mundipharma: Honoraria, Other: Speakers Bureau and/or Advisory Boards, Research Funding; Janssen: Honoraria, Other: Speakers Bureau and/or Advisory Boards, Research Funding; Gilead: Honoraria, Other: Speakers Bureau and/or Advisory Boards, Research Funding. Ghia:Janssen Pharmaceuticals: Research Funding.
Chronic Lymphocytic Leukemia Patients with IGHV Genes Carrying Only Silent Mutations Have A Longer Time From Diagnosis to Initial Therapy Than Patients Expressing B-Cell Receptors with No Somatic Mutations
Kaufman, Matthew, Yan, Xiao‐Jie , Rassenti, Laura Z., Oscier, David , Davi, Frédéric , Belessi, Chrysoula, Davis, Zadie , Byrd, John C. , Brown, Jennifer R. , Rai, Kanti R., Ghia, Emanuela M. , Neuberg, Donna , Σταματόπουλος, Κώστας , Ghia, Paolo , Rosenquist, Richard , Agathangelidis, Andreas , Kay, Neil E. , Rai, Kanti R., Kipps, Thomas J. , Chiorazzi, Nicholas

Blood | October 14, 2019 | Volume: 118 | Issue: 21 | Pages: 288-288

10.1182/blood.v118.21.288.288 Get It

Abstract Abstract 288 BACKGROUND. Chronic lymphocytic leukemia (CLL) patients with mutated IGHV genes (M-CLL) have better outcomes than patients with unmutated IGHV genes (U-CLL). It has been proposed that this difference reflects the fact that IGHV mutations alter the structure of the B-cell antigen receptor (BCR) such that it no longer binds stimulatory (auto) antigens and therefore cannot deliver trophic signals to the leukemic cells. For this theory to be correct, only replacement (R) mutations and in particular non-conservative R mutations that would more likely alter amino structure of the IGHV/D/J rearrangements would have relevance. Silent (S) mutations by definition do not change amino acid structure and could not alter antigen binding. We sought to investigate this hypothesis by analyzing the types (S, conservative R, non-conservative R) and distribution of mutations that occur in IGHVs of M-CLL clones and then comparing the time to first therapy (TTFT) in patients with different IGHV features. This analysis expanded an initial study of 1569 CLL cases in the US to include 1858 patients from Europe for a total of 3427 cases. METHODS. Using IGMT software and tools, we analyzed the rearranged IGHV sequences of 3427 cases and characterized their mutations in several respects: first, if IGHV mutations altered amino acid structure (S vs. R); second, if mutations occurred in CDRs (antigen binding domains) or FRs (scaffolds of the BCR); third, if R mutations were conservative or non-conservative as determined by charge, hydropathy, and size. TTFT for patients was examined with various combinations of the above parameters. Differences in TTFT were estimated by the method of Kaplan and Meier and assessed using the log rank test. RESULTS. First, TTFT was compared for 4 groups of patients with the following mutation profiles: no mutations; only S mutations (median 1 per sample); only R mutations (median 1 per sample); and mixed S and R mutations (median 16 per sample). These 4 categories were significantly different (P<0.0001), with the median TTFT being 2.0 yrs for no mutations; 2.6 yrs for R only; 2.8 yrs for S only; and 7.3 yrs for mixed. All comparisons used patients with no mutations (n=1234) as the reference group. We identified statistically longer TTFT (2.8 vs 2.0 yrs; P=0.04) in patients with only S mutations (n=62). Patients with only R mutations (n=218) also had superior outcomes (2.6 yrs vs. 2.0 yrs; P=0.008). There was no statistical significance in TTFT between patients with all S vs. all R mutations (2.8 yrs vs. 2.6 yrs; P=0.71). Because exploring the relevance of BCR structural change on TTFT required us to focus on a small subset of patients with only silent IGHV mutations, our sample size was small. Therefore, we expanded the group to include IGHVs with R mutations limited to the FR region (S + R in FR only; n=241) since these mutations would be unlikely to have a major impact on BCR structure, particularly sparing the binding site. When compared to patients with no mutations, this group demonstrated a significantly longer TTFT (2.8 yrs vs. 2.0 yrs, P=0.0002). This finding was upheld when not permitting any non-conservative R mutations in this group, leaving only patients with S plus conservative R mutations in FRs only (n=124); TTFT in this case was 2.8 yrs vs. 2.0 yrs, respectively (P=0.0006). CONCLUSIONS. Our findings show that patients with only S mutations have better outcomes than patients with no mutations, suggesting that a change in BCR structure that could lead to a loss of antigen binding is an unlikely reason for improved clinical course. This is further supported by the finding that the combination of only S plus conservative R mutations located solely in FRs, which probably would not result in major BCR structural changes and therefore antigen binding, is associated with a lengthened TTFT. Therefore, we suggest that the currently accepted paradigm to explain the enhanced survival of M-CLL patients needs to be re-evaluated. Disclosures: Brown: Calistoga: Consultancy, Research Funding; Celgene: Honoraria, Research Funding; Genzyme: Research Funding; GSK: Research Funding. Kipps:Igenica: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Research Funding; Abbott Industries: Research Funding; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees; Genentech: Research Funding; GSK: Research Funding; Gilead Sciences: Consultancy, Research Funding; Amgen: Research Funding.
Improved Outcome of CLL Patients with Leukemic Clones Expressing Mutated IGHV May Not Be Due to An Inability to Bind (auto)Antigen In Vivo
Kaufman, Matthew, Yan, Xiao‐Jie , Rassenti, Laura Z., Brown, Jennifer R. , Byrd, John C. , Rai, Kanti R, Ghia, Emanuela M. , Neuberg, Donna , Kay, Neil E. , Rai, Kanti R, Kipps, Thomas J. , Chiorazzi, Nicholas

Blood | October 11, 2019 | Volume: 116 | Issue: 21 | Pages: 2441-2441

10.1182/blood.v116.21.2441.2441 Get It

Abstract Abstract 2441 Background: CLL patients with mutated IGHVs (M-CLL) have clinical outcomes better than patients with unmutated BCRs (U-CLL). It is believed that this difference stems from the fact that somatic mutations have altered the structure of the BCR such that it no longer binds stimulatory (auto)antigens and therefore cannot deliver trophic signals to the leukemic cells. We sought to determine if this belief could be corroborated by analyzing the types (silent vs. conservative vs. non-conservative) and locations (FRs v CDRs) of mutations that occurred in IGHVs of M-CLL clones and then comparing the time to first therapy (TTFT) in patients with different IGHV features. Methods: Using IGMT software, we analyzed the IGHV sequences of 1560 cases and characterized their mutations in several respects: first, if IGHV mutations altered amino acid structure (silent vs. replacement); second, if mutations occurred in CDRs (antigen binding domains) or FRs (scaffolds of the BCR); third, if mutations were conservative or non-conservative (as determined by charge, hydropathy, size). TTFT for patients was correlated with various combinations of the above parameters. Differences in TTFT were estimated by the method of Kaplan and Meier; differences were assessed using the log rank test. Results: First we compared TTFT in patients who had only silent mutations (n=32) to those with no mutations (n=563) and found a trend toward longer TTFT in patients with silent mutations (3.0 vs. 3.6 yrs, p=0.09). Because the statistical significance of this result was likely influenced by the small numbers of clones with only silent mutations, we expanded the group to include IGHVs with replacement mutations of only the conservative type (n=83) since these would be unlikely to havemajor impact on BCR structure. Comparison of this group with those with no mutations for differences in TTFT was significant (3.0 vs. 3.9 yrs, p=0.0007). Furthermore, comparisons of patients with silent plus conservative mutations in FRs only (n=123) versus patients with no mutations showed a clear difference in TTFT (3.0 vs. 4.1, respectively; (p<0.003). In both of the above instances, non-conservative replacement mutations do not have a significantly greater impact on TTFT than the silent plus conservative combination. Conclusions: It is assumed that M-CLL patients have a clinical course superior to U-CLL patients because IGHV somatic mutations change the structure of the M-CLL BCR such that it no longer binds stimulatory antigens. For this theory to be correct, only replacement mutations and in particular non-conservative replacement mutations that would alter amino structure of the IGHV/D/J rearrangements would have relevance. Silent mutations, which by definition do not change amino acid structure, should be irrelevant in this regard, and conservative mutations, which substitute amino acids with similar chemical properties to the original amino acid, would be unlikely to result in major changes in the BCR. Therefore, the fact that the combination of only silent plus conservative mutations, which probably would not result in changes in BCR structure and therefore antigen binding, is associated with a lengthened TTFT militates against a loss of antigen binding as a reason for improved clinical course. Therefore, we suggest that another explanation for the enhanced survival of M-CLL patients should be sought. One possibility is that the cells that have the capacity to mutate their IGHVs are different in origin and/or biologic properties from those that cannot, and these account for the differences in survival between M- and U-CLL patients. (This work was supported NIH grant PO1-CA81534 of the CLL Research Consortium.) Disclosures: Byrd: Genzyme Corporation: Research Funding. Kipps: GlaxoSmithKline: Research Funding.
Reappraising Immunoglobulin Repertoire Restrictions in Chronic Lymphocytic Leukemia: Focus on Major Stereotyped Subsets and Closely Related Satellites
Hadzidimitriou, Anastasia , Minga, Eva, Sutton, Lesley‐Ann, Polychronidou, Eleftheria, Davis, Zadie , Yan, Xiao‐Jie , Boudjoghra, Myriam, Pedersen, Lone Bredo , Bikos, Vasilis, Xochelli, Aliki , Celle, Paola Francia di, Evers, Ludo M., Facco, Monica , Moschonas, Panagiotis, Bystrý, Vojtěch , Roumelioti, Maria, Pavlović, Sonja , Mansouri, Larry, Chu, Charles C. , Sudarikov, Andrey , Catherwood, Mark , Montillo, Marco , Stavroyianni, Niki, Pospı́šilová, Šárka , Lefranc, Marie‐Paule , Jaeger, Ulrich, Kater, Arnon P. , Pott, Christiane , Oscier, David , Jelinek, Diane F., Hallek, Michael , Darzentas, Nikos , Belessi, Chrysoula, Davi, Frédéric , Agathangelidis, Andreas , Shanafelt, Tait D. , Plevová, Karla , Navarro, Alba , Rossi, Davide , Baliakas, Panagiotis , Scarfò, Lydia , Mattsson, Mattias , Giannopoulos, Krzysztof , Vanura, Katrina , Veronese, Silvio , Karan-Djurašević, Teodora , Stalika, Evangelia , Giudicelli, Véronique , Panagiotidis, Panagiotis T. , Anagnostopoulos, Αchilles , Trentin, Livio , Gaïdano, Gianluca , Campo, Elı́as , Niemann, Carsten Utoft , Langerak, Anton W. , Chiorazzi, Nicholas , Stilgenbauer, Stephan , Tzovaras, Dimitrios K. , Rosenquist, Richard , Ghia, Paolo , Σταματόπουλος, Κώστας

Blood | October 11, 2019 | Volume: 128 | Issue: 22 | Pages: 4376-4376

10.1182/blood.v128.22.4376.4376 Get It

Abstract The existence of stereotyped B cell receptor immunoglobulins (BcR IG) in chronic lymphocytic leukemia (CLL) strongly implicated antigen selection in disease ontogeny. We have previously shown that the stereotyped fraction encompasses ~30% of all CLL and includes multiple subsets with distinct BcR IG configuration and variable size. Eventually, certain major subsets emerged as distinct clinical entities, exemplified by subset #2 (IGHV3-21/IGLV3-21, ~2.5-3% of all CLL, mixed somatic hypermutation (SHM) status) of a particularly aggressive clinical course, thus, sharply contrasting subset #4 (IGHV4-34/IGKV2-30, ~1% of all CLL, mutated IGHV genes, M-CLL), a prototype for indolent disease. Here, taking advantage of a multi-institutional cohort of 21,123 CLL IG rearrangements, almost three times the size of the largest previous study, and the availability of validated, purpose-built immunoinformatics methods, we reappraised BcR IG stereotypy especially focusing on major subsets and the degree of their sequence similarity to related minor subsets. Stereotypy discovery was performed with ARResT/Teiresias, while stereotypy assignment to existing subsets previously deemed as major was performed with ARResT/AssignSubsets (http://bat.infspire.org/arrest/). In the present study, a subset was characterized as major if representing > 0.2% of the cohort (i.e. at least 50 cases). Minor subsets closely related to major ones (termed satellite) were identified applying the following criteria: (i) usage of IGHV genes from the same phylogenetic clan; (ii) VH CDR3 length difference ranging from -2 to +2 compared to the respective major subset; (iii) shared VH CDR3 sequence motif; and, (iv) -2 to +2 difference in the offset of the VH CDR3 motif compared to the respective major subset. In total, 7378/21123 (34.9%) IG sequences were grouped into subsets with stereotyped VH CDR3, with the previously characterized 19 major subsets accounting collectively for 2594 sequences (12.3%) of the cohort: of these, 12 included cases with unmutated IGHV genes (U-CLL), 6 concerned M-CLL and 1 (subset #2) included cases with mixed SHM status. Four additional subsets exceeded 50 cases, and, thus, were also considered as 'major'. These results reinforce the notion that not all CLL will end up being stereotyped but rather that a plateau for stereotypy exists at ~1/3 of the cohort. Subset #2 was the largest subset (n=572, 2.7%), while subset #1 (IGHV clan I (IGHV1,5,7 subgroups)/IGKV1(D)-39) was the most frequent subset within U-CLL (n=515, 2.4%) and subset #4 the most common M-CLL subset (n=192, 0.9%), hence displaying remarkable consistency regarding their frequency in all cohorts published since the pioneering studies. Altogether, Teiresias and AssignSubsets gave concordant results for previously identified major subsets, illustrating the validity of our approach. Satellite subsets were sought for individually for each major subset. In general, few satellite subsets were identified, most of which concerned U-CLL major subsets. That notwithstanding, notable cases of satellite subsets were exemplified by major subset #1 and its satellite subset #99 from which it differed only in VH CDR3 length (13 aminoacids in subset #1 versus 14 in subset #99); interestingly, both subsets displayed equally aggressive clinical course. Another example concerned subset #8 (IGHV4-39/IGKV1(D)-39, U-CLL), an aggressive subset with very high risk for Richter's transformation, that, except for a one-aminoacid difference in VH CDR3 length, was otherwise identical to satellite subset #215, also displaying clinical aggressiveness. Overall, our results confirm that major subsets can be robustly identified and are consistent in relative size, hence representing distinct disease subgroups amenable to compartmentalized research with the potential of overcoming the pronounced heterogeneity of CLL. Most major subsets display unique sequence motifs, however satellite subsets exist, especially within U-CLL. Considering ever-increasing evidence that major stereotyped subsets may represent distinct disease subgroups, the existence of satellite subsets reveals a novel aspect of repertoire restriction and has implications for refined molecular classification of CLL. Disclosures Shanafelt: Genentech: Research Funding; GlaxoSmithkKine: Research Funding; Celgene: Research Funding; Janssen: Research Funding; Pharmacyclics: Research Funding; Cephalon: Research Funding; Hospira: Research Funding. Gaidano:Roche: Consultancy, Honoraria, Speakers Bureau; Karyopharm: Consultancy, Honoraria; Morphosys: Consultancy, Honoraria; Gilead: Consultancy, Honoraria, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Novartis: Consultancy, Honoraria, Speakers Bureau. Niemann:Janssen: Consultancy; Abbvie: Consultancy; Roche: Consultancy; Gilead: Consultancy. Langerak:F. Hofmann-LaRoche, Genentech: Research Funding; InVivoScribe Technologies: Patents & Royalties: Royalties are provided to European Network (EuroClonality). Jaeger:Roche: Honoraria, Research Funding; Celgene: Honoraria, Research Funding. Kater:Celgene: Research Funding; Gilead: Research Funding; Janssen: Consultancy, Research Funding; Roche: Consultancy, Research Funding; Abbvie: Consultancy, Research Funding. Stilgenbauer:Amgen: Consultancy, Honoraria, Other: Travel grants, Research Funding; Gilead: Consultancy, Honoraria, Other: Travel grants , Research Funding; Genentech: Consultancy, Honoraria, Other: Travel grants , Research Funding; Celgene: Consultancy, Honoraria, Other: Travel grants , Research Funding; Boehringer Ingelheim: Consultancy, Honoraria, Other: Travel grants , Research Funding; Genzyme: Consultancy, Honoraria, Other: Travel grants , Research Funding; AbbVie: Consultancy, Honoraria, Other: Travel grants, Research Funding; GSK: Consultancy, Honoraria, Other: Travel grants , Research Funding; Janssen: Consultancy, Honoraria, Other: Travel grants , Research Funding; Mundipharma: Consultancy, Honoraria, Other: Travel grants , Research Funding; Novartis: Consultancy, Honoraria, Other: Travel grants , Research Funding; Pharmacyclics: Consultancy, Honoraria, Other: Travel grants , Research Funding; Hoffmann-La Roche: Consultancy, Honoraria, Other: Travel grants , Research Funding; Sanofi: Consultancy, Honoraria, Other: Travel grants , Research Funding. Hallek:Gilead: Consultancy, Honoraria, Other: travel support, Research Funding, Speakers Bureau; F. Hoffmann-LaRoche: Consultancy, Honoraria, Other: travel support, Research Funding, Speakers Bureau; Mundipharma: Consultancy, Honoraria, Other: travel support, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Other: travel support, Research Funding, Speakers Bureau; AbbVie: Consultancy, Honoraria, Other: travel support, Research Funding, Speakers Bureau; Janssen-Cilag: Consultancy, Honoraria, Other: travel support, Research Funding, Speakers Bureau; Amgen: Consultancy, Honoraria, Other: travel support, Research Funding, Speakers Bureau. Rosenquist:Gilead Sciences: Speakers Bureau. Ghia:Gilead: Consultancy, Honoraria, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Roche: Honoraria, Research Funding; Adaptive: Consultancy; Abbvie: Consultancy, Honoraria. Stamatopoulos:Novartis: Honoraria, Research Funding; Abbvie: Honoraria, Other: Travel expenses; Janssen: Honoraria, Other: Travel expenses, Research Funding; Gilead: Consultancy, Honoraria, Research Funding.